An assembly graph tangle resulting from the rDNA arrays of the HG002 human genome. Bandage (Wick et al. 2015) visualization of the assembly graph for the 10 HG002 acrocentric chromosomes (diploid Chromosomes 13, 14, 15, 21, 22). Maternal and paternal haplotype–assigned nodes are shown in red and blue, respectively; the rDNA repeats, in light green; the distal satellite regions, in orange; and the telomeres, in dark green. Each distal satellite is labeled according to the HG002 v1.0.1 reference assembly, with the exception of Chromosome 13 and Chromosome 22 paternal, which are too similar to be separated (Potapova et al. 2024).The inset shows a linear schematic of a human acrocentric chromosome with colors matching the assembly graph. The paternal and maternal haplotype–assigned sequences comprise the entire q-arm and the proximal component of the p-arm. In the contrast to other regions of the genome, the short arms of the acrocentric chromosomes do not split into a typical diploid arrangement and are difficult to phase correctly. Such complex structures violate common assumptions made by diploid phasing and scaffolding tools.
